gmod-ajax — JBrowse list

Re: [Gmod-ajax] url template

[David B. <dav...@gm...>]

I take my question back.
--urltemplate "http://www.google.com/search?q={id}" works fine.

On Mon, Aug 9, 2010 at 10:21 AM, David Breimann <dav...@gm...>wrote:

> Hello,
>
> I am adding features from GFF3 using flatfile-to-json.pl. I would like to
> add a url template that refers to http://some_url_here/xxx, where xxx is
> the ID of the feature.
> How can I do that? Do I have to write a config file myself?
>
> Thanks
> Dave
>

[Gmod-ajax] url template

[David B. <dav...@gm...>]

Hello,

I am adding features from GFF3 using flatfile-to-json.pl. I would like to
add a url template that refers to http://some_url_here/xxx, where xxx is the
ID of the feature.
How can I do that? Do I have to write a config file myself?

Thanks
Dave

Re: [Gmod-ajax] I give up. What is the magic to get subfeatures?

[Paul S. <pau...@gm...>]

Using --gff instead of --gff2 helps too. Thanks.

On Fri, Aug 6, 2010 at 1:51 PM, Mitch Skinner
<mit...@be...> wrote:
>  And once you've made the modifications that Scott recommends, it may help
> to change the --gff2 parameter to --gff.  In this case, "--gff" means GFF3.
>  When I wrote that code, I guess I was thinking of GFF3 as being the typical
> version of GFF.  GFF3 was the first version JBrowse supported, anyway, and
> when I added a separate code path for GFF2 then I added the --gff2
> parameter.
>
> It's like the first part of the flatfile-to-json.pl usage message says:
>
> USAGE: bin/flatfile-to-json.pl [--gff <gff3 file> | --gff2 <gff2 file> |
> --bed <bed file>]
>
> Sorry for any confusion,
> Mitch
>
> On 08/06/2010 09:05 AM, Paul Stodghill wrote:
>>
>> ##gff-version 3
>> NC_004578       GenBank gene    8438    15223   .       +       1
>> ID=1489763;
>> NC_004578       GenBank CDS     9000    10000   .       +       1
>> ID=9695423; Parent:1489763;
>> NC_004578       GenBank CDS     11000   12000   .       +       1
>> ID=9695424; Parent:1489763;
>>
>> Here is how I am invoking  flatfile-to-json.pl,
>>
>> ./bin/flatfile-to-json.pl --gff2 test.gff --getType --getSubs
>> --tracklabel test --key test --subfeatureClasses '{"CDS":
>> "transcript-CDS"}'
>>
>
>

Re: [Gmod-ajax] I give up. What is the magic to get subfeatures?

[Paul S. <pau...@gm...>]

That helped. With this new GFF file,

##gff-version 3
NC_004578	GenBank	gene	8438	15223	.	+	1	ID=1489763
NC_004578	GenBank	CDS	9000	10000	.	+	1	Parent=1489763
NC_004578	GenBank	CDS	11000	12000	.	+	1	Parent=1489763

and this command,

./bin/flatfile-to-json.pl --gff test.gff \
    --getType --getSubs --tracklabel test --key test \
    --subfeatureClasses '{"CDS": "transcript-CDS"}'

I am closer to the resutls that I want.

Thank you.

On Fri, Aug 6, 2010 at 1:10 PM, Scott Cain <sc...@sc...> wrote:
> Hi Paul,
>
> Off hand, I don't know the details of JBrowse configuration, but I can
> tell you that you GFF is wrong.  The Parent part should look like the
> ID part, with tag=value, so the ninth column should look like this
> "ID=9695423;Parent=1489763".  Also, there is no need for the CDS
> features to have an ID unless those features have children as well;
> IDs are only for identifying parent-child relationships.  You might
> find the GFF3 validator useful:
>
>  http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online
>
> Scott
>
>
> On Fri, Aug 6, 2010 at 12:05 PM, Paul Stodghill
> <pau...@gm...> wrote:
>> I'm trying to create a feature track that contains nested features,
>> similar to the mRNA track in the Drosophila.
>>
>> Here is the GFF file that I am using as input,
>>
>> ##gff-version 3
>> NC_004578       GenBank gene    8438    15223   .       +       1       ID=1489763;
>> NC_004578       GenBank CDS     9000    10000   .       +       1       ID=9695423; Parent:1489763;
>> NC_004578       GenBank CDS     11000   12000   .       +       1       ID=9695424; Parent:1489763;
>>
>> Here is how I am invoking  flatfile-to-json.pl,
>>
>> ./bin/flatfile-to-json.pl --gff2 test.gff --getType --getSubs
>> --tracklabel test --key test --subfeatureClasses '{"CDS":
>> "transcript-CDS"}'
>>
>> I can see that both trackData.json and subfeatures-1.json are being
>> created in the right track directory.
>>
>> Here is what gets inserted into trackInfo.js
>>
>>   {
>>      "url" : "data/tracks/{refseq}/test/trackData.json",
>>      "type" : "FeatureTrack",
>>      "label" : "test",
>>      "key" : "test"
>>   }
>>
>> For starters, I see that "subfeatures":true needs to be added to
>> trackInfo.js, but what else?
>>
>> (I tried following the configuration provided for the Drosophila, but
>> the syntax used for that example and for the for the config file
>> reference documentation appear to be out of sync with the current
>> implementation.)
>>
>> Thanks.
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by
>>
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>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

Re: [Gmod-ajax] I give up. What is the magic to get subfeatures?

[Mitch S. <mit...@be...>]

  On 08/06/2010 09:05 AM, Paul Stodghill wrote:
> For starters, I see that "subfeatures":true needs to be added to
> trackInfo.js, but what else?

"subfeatures": true can go in the config file, yes, but it doesn't end 
up in trackInfo.js, which is something else.

> (I tried following the configuration provided for the Drosophila, but
> the syntax used for that example and for the for the config file
> reference documentation appear to be out of sync with the current
> implementation.)

I'm not sure what specifically you're referring to here, but I'm 
guessing that there may be some confusion related to the roles that the 
different JS(ON) files play in JBrowse.

For biodb-to-json.pl, it goes:

JSON config file--->biodb-to-json.pl--->(one entry in data/trackInfo.js, 
data/tracks/<refseq>/<tracklabel>/trackData.json, optionally 
data/tracks/<refseq>/<tracklabel>/subfeatures-*.json)

for flatfile-to-json.pl, it goes:

command line parameters--->flatfile-to-json.pl--->(one entry in 
data/trackInfo.js, data/tracks/<refseq>/<tracklabel>/trackData.json, 
optionally data/tracks/<refseq>/<tracklabel>/subfeatures-*.json)

So the config file looks different from (and serves a different role 
from) data/trackInfo.js.  The config file tells biodb-to-json.pl how to 
generate the JSON for each track; trackInfo.js tells the client-side 
javascript what tracks are available.

Regards,
Mitch

Re: [Gmod-ajax] I give up. What is the magic to get subfeatures?

[Mitch S. <mit...@be...>]

  And once you've made the modifications that Scott recommends, it may 
help to change the --gff2 parameter to --gff.  In this case, "--gff" 
means GFF3.  When I wrote that code, I guess I was thinking of GFF3 as 
being the typical version of GFF.  GFF3 was the first version JBrowse 
supported, anyway, and when I added a separate code path for GFF2 then I 
added the --gff2 parameter.

It's like the first part of the flatfile-to-json.pl usage message says:

USAGE: bin/flatfile-to-json.pl [--gff <gff3 file> | --gff2 <gff2 file> | 
--bed <bed file>]

Sorry for any confusion,
Mitch

On 08/06/2010 09:05 AM, Paul Stodghill wrote:
> ##gff-version 3
> NC_004578	GenBank	gene	8438	15223	.	+	1	ID=1489763;
> NC_004578	GenBank	CDS	9000	10000	.	+	1	ID=9695423; Parent:1489763;
> NC_004578	GenBank	CDS	11000	12000	.	+	1	ID=9695424; Parent:1489763;
>
> Here is how I am invoking  flatfile-to-json.pl,
>
> ./bin/flatfile-to-json.pl --gff2 test.gff --getType --getSubs
> --tracklabel test --key test --subfeatureClasses '{"CDS":
> "transcript-CDS"}'
>

Re: [Gmod-ajax] I give up. What is the magic to get subfeatures?

[Scott C. <sc...@sc...>]

Hi Paul,

Off hand, I don't know the details of JBrowse configuration, but I can
tell you that you GFF is wrong.  The Parent part should look like the
ID part, with tag=value, so the ninth column should look like this
"ID=9695423;Parent=1489763".  Also, there is no need for the CDS
features to have an ID unless those features have children as well;
IDs are only for identifying parent-child relationships.  You might
find the GFF3 validator useful:

  http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online

Scott


On Fri, Aug 6, 2010 at 12:05 PM, Paul Stodghill
<pau...@gm...> wrote:
> I'm trying to create a feature track that contains nested features,
> similar to the mRNA track in the Drosophila.
>
> Here is the GFF file that I am using as input,
>
> ##gff-version 3
> NC_004578       GenBank gene    8438    15223   .       +       1       ID=1489763;
> NC_004578       GenBank CDS     9000    10000   .       +       1       ID=9695423; Parent:1489763;
> NC_004578       GenBank CDS     11000   12000   .       +       1       ID=9695424; Parent:1489763;
>
> Here is how I am invoking  flatfile-to-json.pl,
>
> ./bin/flatfile-to-json.pl --gff2 test.gff --getType --getSubs
> --tracklabel test --key test --subfeatureClasses '{"CDS":
> "transcript-CDS"}'
>
> I can see that both trackData.json and subfeatures-1.json are being
> created in the right track directory.
>
> Here is what gets inserted into trackInfo.js
>
>   {
>      "url" : "data/tracks/{refseq}/test/trackData.json",
>      "type" : "FeatureTrack",
>      "label" : "test",
>      "key" : "test"
>   }
>
> For starters, I see that "subfeatures":true needs to be added to
> trackInfo.js, but what else?
>
> (I tried following the configuration provided for the Drosophila, but
> the syntax used for that example and for the for the config file
> reference documentation appear to be out of sync with the current
> implementation.)
>
> Thanks.
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] I give up. What is the magic to get subfeatures?

[Paul S. <pau...@gm...>]

I'm trying to create a feature track that contains nested features,
similar to the mRNA track in the Drosophila.

Here is the GFF file that I am using as input,

##gff-version 3
NC_004578	GenBank	gene	8438	15223	.	+	1	ID=1489763;
NC_004578	GenBank	CDS	9000	10000	.	+	1	ID=9695423; Parent:1489763;
NC_004578	GenBank	CDS	11000	12000	.	+	1	ID=9695424; Parent:1489763;

Here is how I am invoking  flatfile-to-json.pl,

./bin/flatfile-to-json.pl --gff2 test.gff --getType --getSubs
--tracklabel test --key test --subfeatureClasses '{"CDS":
"transcript-CDS"}'

I can see that both trackData.json and subfeatures-1.json are being
created in the right track directory.

Here is what gets inserted into trackInfo.js

   {
      "url" : "data/tracks/{refseq}/test/trackData.json",
      "type" : "FeatureTrack",
      "label" : "test",
      "key" : "test"
   }

For starters, I see that "subfeatures":true needs to be added to
trackInfo.js, but what else?

(I tried following the configuration provided for the Drosophila, but
the syntax used for that example and for the for the config file
reference documentation appear to be out of sync with the current
implementation.)

Thanks.

Re: [Gmod-ajax] concurrent?

[Mitch S. <mit...@be...>]

  The scripts do take locks when they're updating the JSON; I've run 
them concurrently on a number of occasions but I've never really 
torture-tested them.

Mitch

On 08/05/2010 03:10 AM, David Breimann wrote:
> Hi,
>
> Many time I go through the routine of adding a sequence file, adding 
> features from multiple GFF3 files than adding multiple numeric tracks 
> from WIG files.
> I have a script that does all that, but it works serially and it takes 
> a good minute or two.
> Do you think it's possible to run some of the things concurrently?
> For example, I obviously have to add the sequence before anything 
> else, but maybe I can add multiple tracks at the same time?
> So, do you think it's safe to run multiple ..-to-json.pl 
> <http://to-json.pl> or are there any shared resources they might try 
> to update simultaneously and cause errors?
>
> Thanks,
> Dave
>
>
> ------------------------------------------------------------------------------
> The Palm PDK Hot Apps Program offers developers who use the
> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
> of $1 Million in cash or HP Products. Visit us here for more details:
> http://p.sf.net/sfu/dev2dev-palm
>
>
> _______________________________________________
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[Gmod-ajax] concurrent?

[David B. <dav...@gm...>]

Hi,

Many time I go through the routine of adding a sequence file, adding
features from multiple GFF3 files than adding multiple numeric tracks from
WIG files.
I have a script that does all that, but it works serially and it takes a
good minute or two.
Do you think it's possible to run some of the things concurrently?
For example, I obviously have to add the sequence before anything else, but
maybe I can add multiple tracks at the same time?
So, do you think it's safe to run multiple ..-to-json.pl or are there any
shared resources they might try to update simultaneously and cause errors?

Thanks,
Dave

Re: [Gmod-ajax] Formatting using GFF notes and some other stuff

[David B. <dav...@gm...>]

I think that different setups can be achieved using the "link", but cleaning
things up can't be done (unless clearing the browser's history).

On Thu, Aug 5, 2010 at 1:14 AM, Mitch Skinner <mit...@be...>wrote:

>  The reason I asked is because I want to know why you want to start over
> from scratch.  For example, if you're usually switching between two
> different tasks, then maybe it would be better to implement a mechanism to
> enable the user to switch between different track setups, rather than making
> the user recreate their setup on each switch.  Which is something that other
> people (Andrew Uzilov, for example) have suggested.
>
> Mitch
>
>
> On 07/30/2010 10:25 AM, David Breimann wrote:
>
> That;s wired, those mess sages never reached me.
> Regarding the default view: it just that I'm working with many tracks, and
> sometimes I like to "clean" things up and start from scratch. Then  simply
> remove them all manually" (drag each track out of the view), but then the
> list of tracks is a mess (initially, I create it ordered by some logic).
> Obviously, some kind of track hierarchy or grouping (like in GBrowse) would
> be even better).
>
> And thank you for the replies.
>
> On Fri, Jul 30, 2010 at 7:59 PM, Mitch Skinner <mit...@be...
> > wrote:
>
>> On 07/30/2010 06:37 AM, David Breimann wrote:
>>
>>> Well, I also always use 0-based coordinates when I program (as is the
>>> rule for arrays in java, perl etc.), but for the user interface - I think
>>> it's better show coordinates starting from 1 (as is the rule in all
>>> biological databases). For example, when looking at some gene of interest, I
>>> think the user expects to see the same coordinates as will be shown in
>>> genbank, UCSC genome browser etc. Otherwise, this might cause confusion.
>>>
>>
>>  I've slowly come around to thinking that we will have to support this
>> unfortunate convention.  UCSC does the same thing; everything is interbase
>> except the numbers that it shows people.  Hopefully we can isolate this
>> weirdness to one part of the code, and not have " + 1" sprinkled all over
>> the place.b
>>
>>
>>  Also, I will appreciate a response for my previous message (cluases 1-5,
>>> below).
>>>
>>
>>  A few days ago:
>>
>> http://gmod.827538.n3.nabble.com/Gmod-ajax-Formatting-using-GFF-notes-and-some-other-stuff-tp998491p999264.html
>>
>> Mitch
>>
>
>
>

[Gmod-ajax] GMOD Europe 2010 Registration Now Open

[Dave C. G. H. D. <he...@gm...>]

GMOD Europe 2010
================
13-16 September 2010
Cambridge, UK
http://gmod.org/wiki/GMOD_Europe_2010


We are pleased to announce GMOD Europe 2010, four days of GMOD events being
held 13-16 September 2010, at the University of Cambridge. GMOD Europe 2010
includes:

1) GMOD Community Meeting, Monday & Tuesday:  Project updates, developer and
user presentations and best practices, project direction.

2) GMOD Satellite Meetings, Wednesday:  Special interest groups where GMOD
community members meet to discuss specific topics of interest.

3) InterMine Workshop, Wednesday:  A one day workshop on installing,
configuring and using the InterMine biological data warehouse system.

4) BioMart Workshop, Thursday:  A one day workshop on using the BioMart
biological data warehouse system, including accessing data through APIs.

Registration is now open for these events. There is a £50 registration fee
for the GMOD Meeting to cover catered lunches, coffee/tee breaks, and other
expenses. Registration for all other events is free, but still required, as
space is limited.

These events are open to all: GMOD users, developers, prospective users,
biologists, and computer scientists.  For an idea of what goes on at GMOD
meetings, see http://gmod.org/wiki/January_2010_GMOD_Meeting.

See you in Cambridge!

Scott Cain and Dave Clements


PS: If you have topics you want to have covered (or you want to cover) at
the GMOD Meeting, or at the Satellite Meetings, please add them to the wiki
pages, or contact us. We are also asking for guest speaker nominations for
the meeting.
-- 
http://gmod.org/wiki/GMOD_News
<http://gmod.org/wiki/GMOD_News>http://gmod.org/wiki/GMOD_Evo_Hackathon
http://gmod.org/wiki/GMOD_Europe_2010
http://gmod.org/wiki/Help_Desk_Feedback

Re: [Gmod-ajax] [Gmod-gbrowse] deprecate GBrowse for JBrowse?

[Dave C. G. H. D. <he...@gm...>]

Hi Erick,

I know that Scott and I will be at the September meeting.  I don't know if
Lincoln, Ian Holmes, or Mitch Skinner will be there.

This sounds like an excellent topic for the meeting.  I've added it to the
agenda suggestions (
http://gmod.org/wiki/September_2010_GMOD_Meeting#Agenda_Proposals).
 Somebody will talk about this.

Dave C

On Wed, Aug 4, 2010 at 6:51 AM, Erick Antezana <eri...@gm...>wrote:

> Hi Lincoln, Scott,
>
> will that topic (GBrowse deprecation plan) be discussed in the next
> GMOD meeting in Cambridge
> (http://gmod.org/wiki/September_2010_GMOD_Meeting) ? Or in general the
> future of the different GMOD tools? If it will be the case (or not),
> could you please give us some more info about those plans?
>
> cheers,
> Erick
>
> >We plan to deprecate GBrowse for JBrowse over the next couple of years as
> JBrowse continues to mature.
>
> >Lincoln
>
> >On Fri, Jul 2, 2010 at 12:09 PM, Scott Cain <[hidden email]> wrote:
> >    Hi David,
> >    I think what you are asking about is a google maps/ajax type
> >    interface, where the browser asynchronously asks for content before
> >    you do, so that it is just ready to go when you want it.  I don't see
> >    GBrowse 2 getting this sort of functionality, particularly since there
> >    is considerable effort going into having that sort of functionality
> >    for JBrowse.  Have you looked at it?
> >
> >     http://jbrowse.org/
> >
> >    It is not as mature as GBrowse yet, and lacks some of the
> >    functionality of GBrowse, but it is a nice browser.
> >
> >    Scott
>
>
> ------------------------------------------------------------------------------
> The Palm PDK Hot Apps Program offers developers who use the
> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
> of $1 Million in cash or HP Products. Visit us here for more details:
> http://p.sf.net/sfu/dev2dev-palm
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>



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http://gmod.org/wiki/Help_Desk_Feedback

Re: [Gmod-ajax] Formatting using GFF notes and some other stuff

[Mitch S. <mit...@be...>]

  The reason I asked is because I want to know why you want to start 
over from scratch.  For example, if you're usually switching between two 
different tasks, then maybe it would be better to implement a mechanism 
to enable the user to switch between different track setups, rather than 
making the user recreate their setup on each switch.  Which is something 
that other people (Andrew Uzilov, for example) have suggested.

Mitch

On 07/30/2010 10:25 AM, David Breimann wrote:
> That;s wired, those mess sages never reached me.
> Regarding the default view: it just that I'm working with many tracks, 
> and sometimes I like to "clean" things up and start from scratch. 
> Then  simply remove them all manually" (drag each track out of the 
> view), but then the list of tracks is a mess (initially, I create it 
> ordered by some logic).
> Obviously, some kind of track hierarchy or grouping (like in GBrowse) 
> would be even better).
>
> And thank you for the replies.
>
> On Fri, Jul 30, 2010 at 7:59 PM, Mitch Skinner 
> <mit...@be... <mailto:mit...@be...>> wrote:
>
>     On 07/30/2010 06:37 AM, David Breimann wrote:
>
>         Well, I also always use 0-based coordinates when I program (as
>         is the rule for arrays in java, perl etc.), but for the user
>         interface - I think it's better show coordinates starting from
>         1 (as is the rule in all biological databases). For example,
>         when looking at some gene of interest, I think the user
>         expects to see the same coordinates as will be shown in
>         genbank, UCSC genome browser etc. Otherwise, this might cause
>         confusion.
>
>
>     I've slowly come around to thinking that we will have to support
>     this unfortunate convention.  UCSC does the same thing; everything
>     is interbase except the numbers that it shows people.  Hopefully
>     we can isolate this weirdness to one part of the code, and not
>     have " + 1" sprinkled all over the place.b
>
>
>         Also, I will appreciate a response for my previous message
>         (cluases 1-5, below).
>
>
>     A few days ago:
>     http://gmod.827538.n3.nabble.com/Gmod-ajax-Formatting-using-GFF-notes-and-some-other-stuff-tp998491p999264.html
>
>     Mitch
>
>

Re: [Gmod-ajax] Ensembl data

[Ian H. <ih...@be...>]

Mitch has suggested that we prepackage the JSON files generated from
Ensembl and UCSC human annotation data (and possibly other common
datasets) for easy setup. This is in line with what we had planned to do
anyway, so we are going to go ahead and do this.

Suzanna Lewis wrote:
> Gregg Helt has done most of the work needed to obtain UCSC data (we decided to do UCSC first and then Ensembl followed by Chado as third). He would have to  say where things stand at the moment, but I think it would be easier than starting from scratch.
> 
> -S
>  
> On Aug 4, 2010, at 3:39 AM, James Morris wrote:
> 
>> Hello,
>>
>> I am developing a web application for GWAS results in specific  
>> phenotypes.
>>
>> I would like to use JBrowse to allow users to explore the genomic  
>> region surrounding associations.
>>
>> I plan to use the Ensembl database as the main source of data for the  
>> application.
>>
>> I would therefore like to display the Ensembl human reference and some  
>> additional tracks like SNPs and genes in JBrowse.
>>
>> Has somebody already done this and are files available? If this is not  
>> the case would it be difficult to do so or is there an easier solution  
>> such as using data from UCSC?
>>
>> Many thanks,
>>
>> James
>>
>>
>> -- 
>> The Wellcome Trust Sanger Institute is operated by Genome Research 
>> Limited, a charity registered in England with number 1021457 and a 
>> company registered in England with number 2742969, whose registered 
>> office is 215 Euston Road, London, NW1 2BE. 
>>
>> ------------------------------------------------------------------------------
>> The Palm PDK Hot Apps Program offers developers who use the
>> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
>> of $1 Million in cash or HP Products. Visit us here for more details:
>> http://p.sf.net/sfu/dev2dev-palm
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
> 
> 
> ------------------------------------------------------------------------------
> The Palm PDK Hot Apps Program offers developers who use the
> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
> of $1 Million in cash or HP Products. Visit us here for more details:
> http://p.sf.net/sfu/dev2dev-palm
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] Ensembl data

[Suzanna L. <se...@lb...>]

Gregg Helt has done most of the work needed to obtain UCSC data (we decided to do UCSC first and then Ensembl followed by Chado as third). He would have to  say where things stand at the moment, but I think it would be easier than starting from scratch.

-S
 
On Aug 4, 2010, at 3:39 AM, James Morris wrote:

> Hello,
> 
> I am developing a web application for GWAS results in specific  
> phenotypes.
> 
> I would like to use JBrowse to allow users to explore the genomic  
> region surrounding associations.
> 
> I plan to use the Ensembl database as the main source of data for the  
> application.
> 
> I would therefore like to display the Ensembl human reference and some  
> additional tracks like SNPs and genes in JBrowse.
> 
> Has somebody already done this and are files available? If this is not  
> the case would it be difficult to do so or is there an easier solution  
> such as using data from UCSC?
> 
> Many thanks,
> 
> James
> 
> 
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome Research 
> Limited, a charity registered in England with number 1021457 and a 
> company registered in England with number 2742969, whose registered 
> office is 215 Euston Road, London, NW1 2BE. 
> 
> ------------------------------------------------------------------------------
> The Palm PDK Hot Apps Program offers developers who use the
> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
> of $1 Million in cash or HP Products. Visit us here for more details:
> http://p.sf.net/sfu/dev2dev-palm
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> 

Re: [Gmod-ajax] features disappear when zoomed out (bug?)

[David B. <dav...@gm...>]

Works like a charm!

On Wed, Aug 4, 2010 at 5:17 PM, Mitch Skinner <mit...@be...>wrote:

>  On 07/31/2010 12:11 AM, David Breimann wrote:
>
>> Anyway, the problem is that for regions in the wig file I have no data for
>> (e.g. 1001..94999) I sometime see on the track the edges of some
>> (transparent) graphic tile (?) - see upper track on the attached picture.
>>
>
> Some people have mentioned this before, and I didn't know of a good
> solution at the time.  I googled it again, though, and found that there was
> a simple fix, which I have just committed.
>
> I've tested it on firefox and chrome so far, please let me know if it helps
> in your setup.
>
> Mitch
>

Re: [Gmod-ajax] features disappear when zoomed out (bug?)

[Mitch S. <mit...@be...>]

  On 07/31/2010 12:11 AM, David Breimann wrote:
> Anyway, the problem is that for regions in the wig file I have no data 
> for (e.g. 1001..94999) I sometime see on the track the edges of some 
> (transparent) graphic tile (?) - see upper track on the attached picture.

Some people have mentioned this before, and I didn't know of a good 
solution at the time.  I googled it again, though, and found that there 
was a simple fix, which I have just committed.

I've tested it on firefox and chrome so far, please let me know if it 
helps in your setup.

Mitch

[Gmod-ajax] Ensembl data

[James M. <jm...@sa...>]

Hello,

I am developing a web application for GWAS results in specific  
phenotypes.

I would like to use JBrowse to allow users to explore the genomic  
region surrounding associations.

I plan to use the Ensembl database as the main source of data for the  
application.

I would therefore like to display the Ensembl human reference and some  
additional tracks like SNPs and genes in JBrowse.

Has somebody already done this and are files available? If this is not  
the case would it be difficult to do so or is there an easier solution  
such as using data from UCSC?

Many thanks,

James


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

Re: [Gmod-ajax] features disappear when zoomed out (bug?)

[Mitch S. <mit...@be...>]

  It's tough to say what's going on without being able to see it.  If 
you can send a link, or at least put the generated json files up 
somewhere, then I'd have a better chance of understanding what's going on.

Mitch

On 07/31/2010 12:01 AM, David Breimann wrote:
> Hi,
>
> I have a couple of tracks displaying clones mapped to the genome, 
> which I load from a GFF3 file.
> When I zoom in, I can see the feature fine but once I zoom out and the 
> display changes to "clones per x bp" nothing is visible.
> This is not true for my CDS track, where the histogram is shown 
> correctly when zoomed out. The only difference I could think of 
> between the two tracks is that clones are relatively longer than CDS 
> and that clones have larger overlap with each other.
>
> Best,
> Dave
>
>
> ------------------------------------------------------------------------------
> The Palm PDK Hot Apps Program offers developers who use the
> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
> of $1 Million in cash or HP Products. Visit us here for more details:
> http://p.sf.net/sfu/dev2dev-palm
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] wig-to-json.pl error

[David B. <dav...@gm...>]

Solved. The reason for the error was I accently created my wig file using
0-based coordinates (remember our discussion the other day?..)

On Mon, Aug 2, 2010 at 3:41 PM, David Breimann <dav...@gm...>wrote:

> I get the following error when trying to load a variable step wig file
> using wig-to-json.pl:
>
> *** glibc detected *** /var/www/jbrowse/bin/wig2png: free(): invalid next
> size (normal): 0x091efc08 ***
> ======= Backtrace: =========
> /lib/tls/i686/cmov/libc.so.6(+0x6b591)[0x784591]
> /lib/tls/i686/cmov/libc.so.6(+0x6cde8)[0x785de8]
> /lib/tls/i686/cmov/libc.so.6(cfree+0x6d)[0x788ecd]
> /usr/lib/libstdc++.so.6(_ZdlPv+0x21)[0xa03741]
> /usr/lib/libstdc++.so.6(_ZNSs4_Rep10_M_destroyERKSaIcE+0x1d)[0x9dfc2d]
> /usr/lib/libstdc++.so.6(_ZNSsD1Ev+0x4c)[0x9e15dc]
> /var/www/jbrowse/bin/wig2png[0x8054e83]
> /var/www/jbrowse/bin/wig2png[0x804c70e]
> /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe6)[0x72fbd6]
> /var/www/jbrowse/bin/wig2png[0x804ad21]
> ======= Memory map: ========
> 0027e000-002a1000 r-xp 00000000 07:00 262537     /lib/libpng12.so.0.42.0
> 002a1000-002a2000 r--p 00022000 07:00 262537     /lib/libpng12.so.0.42.0
> 002a2000-002a3000 rw-p 00023000 07:00 262537     /lib/libpng12.so.0.42.0
> 0032d000-00340000 r-xp 00000000 07:00 263613     /lib/libz.so.1.2.3.3
> 00340000-00341000 r--p 00012000 07:00 263613     /lib/libz.so.1.2.3.3
> 00341000-00342000 rw-p 00013000 07:00 263613     /lib/libz.so.1.2.3.3
> 003fa000-003fb000 r-xp 00000000 00:00 0          [vdso]
> 004f5000-00519000 r-xp 00000000 07:00 267772     /lib/tls/i686/cmov/
> libm-2.11.1.so
> 00519000-0051a000 r--p 00023000 07:00 267772     /lib/tls/i686/cmov/
> libm-2.11.1.so
> 0051a000-0051b000 rw-p 00024000 07:00 267772     /lib/tls/i686/cmov/
> libm-2.11.1.so
> 0062b000-00646000 r-xp 00000000 07:00 261290     /lib/ld-2.11.1.so
> 00646000-00647000 r--p 0001a000 07:00 261290     /lib/ld-2.11.1.so
> 00647000-00648000 rw-p 0001b000 07:00 261290     /lib/ld-2.11.1.so
> 00719000-0086c000 r-xp 00000000 07:00 267767     /lib/tls/i686/cmov/
> libc-2.11.1.so
> 0086c000-0086d000 ---p 00153000 07:00 267767     /lib/tls/i686/cmov/
> libc-2.11.1.so
> 0086d000-0086f000 r--p 00153000 07:00 267767     /lib/tls/i686/cmov/
> libc-2.11.1.so
> 0086f000-00870000 rw-p 00155000 07:00 267767     /lib/tls/i686/cmov/
> libc-2.11.1.so
> 00870000-00873000 rw-p 00000000 00:00 0
> 00948000-00a31000 r-xp 00000000 07:00 526178
> /usr/lib/libstdc++.so.6.0.13
> 00a31000-00a32000 ---p 000e9000 07:00 526178
> /usr/lib/libstdc++.so.6.0.13
> 00a32000-00a36000 r--p 000e9000 07:00 526178
> /usr/lib/libstdc++.so.6.0.13
> 00a36000-00a37000 rw-p 000ed000 07:00 526178
> /usr/lib/libstdc++.so.6.0.13
> 00a37000-00a3e000 rw-p 00000000 00:00 0
> 00fbd000-00fda000 r-xp 00000000 07:00 263498     /lib/libgcc_s.so.1
> 00fda000-00fdb000 r--p 0001c000 07:00 263498     /lib/libgcc_s.so.1
> 00fdb000-00fdc000 rw-p 0001d000 07:00 263498     /lib/libgcc_s.so.1
> 08048000-0806a000 r-xp 00000000 07:00 19447
> /var/www/jbrowse/bin/wig2png
> 0806a000-0806b000 r--p 00021000 07:00 19447
> /var/www/jbrowse/bin/wig2png
> 0806b000-0806c000 rw-p 00022000 07:00 19447
> /var/www/jbrowse/bin/wig2png
> 091ee000-09563000 rw-p 00000000 00:00 0          [heap]
> b7700000-b7721000 rw-p 00000000 00:00 0
> b7721000-b7800000 ---p 00000000 00:00 0
> b78dc000-b78df000 rw-p 00000000 00:00 0
> b78f0000-b78f2000 rw-p 00000000 00:00 0
> bfd95000-bfdaa000 rw-p 00000000 00:00 0          [stack]
>
>

[Gmod-ajax] wig-to-json.pl error

[David B. <dav...@gm...>]

I get the following error when trying to load a variable step wig file using
wig-to-json.pl:

*** glibc detected *** /var/www/jbrowse/bin/wig2png: free(): invalid next
size (normal): 0x091efc08 ***
======= Backtrace: =========
/lib/tls/i686/cmov/libc.so.6(+0x6b591)[0x784591]
/lib/tls/i686/cmov/libc.so.6(+0x6cde8)[0x785de8]
/lib/tls/i686/cmov/libc.so.6(cfree+0x6d)[0x788ecd]
/usr/lib/libstdc++.so.6(_ZdlPv+0x21)[0xa03741]
/usr/lib/libstdc++.so.6(_ZNSs4_Rep10_M_destroyERKSaIcE+0x1d)[0x9dfc2d]
/usr/lib/libstdc++.so.6(_ZNSsD1Ev+0x4c)[0x9e15dc]
/var/www/jbrowse/bin/wig2png[0x8054e83]
/var/www/jbrowse/bin/wig2png[0x804c70e]
/lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe6)[0x72fbd6]
/var/www/jbrowse/bin/wig2png[0x804ad21]
======= Memory map: ========
0027e000-002a1000 r-xp 00000000 07:00 262537     /lib/libpng12.so.0.42.0
002a1000-002a2000 r--p 00022000 07:00 262537     /lib/libpng12.so.0.42.0
002a2000-002a3000 rw-p 00023000 07:00 262537     /lib/libpng12.so.0.42.0
0032d000-00340000 r-xp 00000000 07:00 263613     /lib/libz.so.1.2.3.3
00340000-00341000 r--p 00012000 07:00 263613     /lib/libz.so.1.2.3.3
00341000-00342000 rw-p 00013000 07:00 263613     /lib/libz.so.1.2.3.3
003fa000-003fb000 r-xp 00000000 00:00 0          [vdso]
004f5000-00519000 r-xp 00000000 07:00 267772     /lib/tls/i686/cmov/
libm-2.11.1.so
00519000-0051a000 r--p 00023000 07:00 267772     /lib/tls/i686/cmov/
libm-2.11.1.so
0051a000-0051b000 rw-p 00024000 07:00 267772     /lib/tls/i686/cmov/
libm-2.11.1.so
0062b000-00646000 r-xp 00000000 07:00 261290     /lib/ld-2.11.1.so
00646000-00647000 r--p 0001a000 07:00 261290     /lib/ld-2.11.1.so
00647000-00648000 rw-p 0001b000 07:00 261290     /lib/ld-2.11.1.so
00719000-0086c000 r-xp 00000000 07:00 267767     /lib/tls/i686/cmov/
libc-2.11.1.so
0086c000-0086d000 ---p 00153000 07:00 267767     /lib/tls/i686/cmov/
libc-2.11.1.so
0086d000-0086f000 r--p 00153000 07:00 267767     /lib/tls/i686/cmov/
libc-2.11.1.so
0086f000-00870000 rw-p 00155000 07:00 267767     /lib/tls/i686/cmov/
libc-2.11.1.so
00870000-00873000 rw-p 00000000 00:00 0
00948000-00a31000 r-xp 00000000 07:00 526178
/usr/lib/libstdc++.so.6.0.13
00a31000-00a32000 ---p 000e9000 07:00 526178
/usr/lib/libstdc++.so.6.0.13
00a32000-00a36000 r--p 000e9000 07:00 526178
/usr/lib/libstdc++.so.6.0.13
00a36000-00a37000 rw-p 000ed000 07:00 526178
/usr/lib/libstdc++.so.6.0.13
00a37000-00a3e000 rw-p 00000000 00:00 0
00fbd000-00fda000 r-xp 00000000 07:00 263498     /lib/libgcc_s.so.1
00fda000-00fdb000 r--p 0001c000 07:00 263498     /lib/libgcc_s.so.1
00fdb000-00fdc000 rw-p 0001d000 07:00 263498     /lib/libgcc_s.so.1
08048000-0806a000 r-xp 00000000 07:00 19447
/var/www/jbrowse/bin/wig2png
0806a000-0806b000 r--p 00021000 07:00 19447
/var/www/jbrowse/bin/wig2png
0806b000-0806c000 rw-p 00022000 07:00 19447
/var/www/jbrowse/bin/wig2png
091ee000-09563000 rw-p 00000000 00:00 0          [heap]
b7700000-b7721000 rw-p 00000000 00:00 0
b7721000-b7800000 ---p 00000000 00:00 0
b78dc000-b78df000 rw-p 00000000 00:00 0
b78f0000-b78f2000 rw-p 00000000 00:00 0
bfd95000-bfdaa000 rw-p 00000000 00:00 0          [stack]

[Gmod-ajax] GMOD Evo Hackathon Open Call for Participation

[Dave C. G. H. D. <he...@gm...>]

We are seeking participants for the GMOD Tools for Evolutionary Biology
Hackathon, held November 8-12, 2010 at the US National Evolutionary
Synthesis Center (NESCent) in Durham, NC.

This hackathon targets three critical gaps in the capabilities of the GMOD
toolbox that currently limit its utility for evolutionary research:
 1. Visualization of comparative genomics data
 2. Visualization of phylogenetic data and trees
 3. Support for population diversity and phenotype data

If you are interested in these areas and have relevant expertise, you are
strongly encouraged to apply.  Relevant areas of expertise include more than
just software development: if you are a GMOD power user, visualization guru,
domain expert (comparative, phylogenetics, population, ...), or
documentation wizard, then your skills are needed!

How To Apply:
Fill out the online application form at http://bit.ly/gmodevohack.
 Applications are due August 25.

About GMOD:
GMOD is an intercompatible suite of open-source software components for
storing, managing, analyzing, and visualizing genome-scale data. GMOD
includes many widely-used software components: GBrowse and JBrowse, both
genome viewers; GBrowse_syn, a comparative genomics viewer; Chado, a generic
and modular database schema; CMap, a comparative map viewer; as well as many
other components including Apollo, MAKER, BioMart, InterMine, and Galaxy.
 We hope to extend the functionality of existing GMOD components, and
integrate new components as well.

About Hackathons:
A hackathon is an intense event at which a group of programmers with
different backgrounds and skills collaborate hands-on and face-to-face to
develop working code that is of utility to the community as a whole. The mix
of people will include domain experts and computer-savvy end-users.

More details about the event, its motivation, organization, procedures, and
attendees, as well as URLs to the hackathon and related websites are
included below.

Sincerely,

The GMOD EvoHack Organizing Committee (and project affiliations as
relevant):

Nicole Washington, Chair (LBNL, modENCODE, Phenote)

Robert Buels (SGN, Chado NatDiv)

Scott Cain (OICR, GMOD)

Dave Clements (NESCent, GMOD)

Hilmar Lapp (NESCent, Phenoscape, Chado NatDiv)

Sheldon McKay (University of Arizona, iPlant, GBrowse_syn)

-----------------------------
About the GMOD Evo HackathonOverviewWe are organizing a hackathon to fill
critical gaps in the capabilities of the Generic Model Organism Database
(GMOD) toolbox that currently limit its utility for evolutionary research.
Specifically, we will focus on tools for 1) viewing comparative genomics
data; 2) visualizing phylogenomic data; and 3) supporting population
diversity data and phenotype annotation.The event will be hosted at NESCent
and bring together a group of about 20+ software developers, end-user
representatives, and documentation experts who would otherwise not meet. The
participants will include key developers of GMOD components that currently
lack features critical for emerging evolutionary biology research,
developers of informatics tools in evolutionary research that lack GMOD
integration, and informatics-savvy biologists who can represent end-user
requirements.

The event will provide a unique opportunity to infuse the GMOD developer
community with a heightened awareness of unmet needs in evolutionary biology
that GMOD components have the potential to fill, and for tool developers in
evolutionary biology to better understand how best to extend or integrate
with already existing GMOD components.
Before the EventDiscussion of ideas and sometimes even design actually
starts well before the hackathon, on mailing lists, wiki pages, and
conference calls set up among accepted attendees.  This advance work lays
the foundation for participants to be productive from the very first day.
 This also means that participants should be willing to contribute some time
in advance of the hackathon itself to participate in this preparatory
discussion.During the EventTypically, hackathon participants use the morning
of the first day of the event to organize themselves into working groups of
between 3 and 6 people, each with a focused implementation objective.  Ideas
and objectives are discussed, and attendees coalesce around the projects in
which they have the most experience or interest.Deliverables / Event ResultsThe
meeting’s attendance, working groups, and outcomes will be fully logged and
documented on the GMOD wiki (http://gmod.org).  Each working group during
the event will typically have its own wiki page, linked from the main
EvoHack page, where it documents its minutes and design notes, and provides
links to the code and documentation it produces.  Also, since GMOD and
NESCent are both committed to open source principles, all code and
documentation produced by participants during the hackathon must be
published under an OSI-approved open source license.  As contributions to
existing GMOD tools, all hackathon products will most likely satisfy this
requirement automatically.NESCentThis event is sponsored by the US National
Evolutionary Synthesis Center (NESCent, http://www.nescent.org) through its
Informatics Whitepapers program (
http://www.nescent.org/informatics/whitepapers.php). NESCent promotes the
synthesis of information, concepts and knowledge to address significant,
emerging, or novel questions in evolutionary science and its applications.
NESCent achieves this by supporting research and education across
disciplinary, institutional, geographic, and demographic boundaries (see
http://www.nescent.org/science/proposals.php).
LinksMain GMOD EvoHack page, and full proposal:
http://gmod.org/wiki/GMOD_Evo_HackathonNESCent: http://www.nescent.org/
GMOD: http://gmod.org
Similar past NESCent events, see: http://hackathon.nescent.org/
GMOD hackathon application:  http://bit.ly/gmodevohack

-- 
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/GMOD_Europe_2010
http://gmod.org/wiki/Help_Desk_Feedback

[Gmod-ajax] features disappear when zoomed out (bug?)

[David B. <dav...@gm...>]

Hi,

I have a couple of tracks displaying clones mapped to the genome, which I
load from a GFF3 file.
When I zoom in, I can see the feature fine but once I zoom out and the
display changes to "clones per x bp" nothing is visible.
This is not true for my CDS track, where the histogram is shown correctly
when zoomed out. The only difference I could think of between the two tracks
is that clones are relatively longer than CDS and that clones have larger
overlap with each other.

Best,
Dave

Re: [Gmod-ajax] Formatting using GFF notes and some other stuff

[David B. <dav...@gm...>]

Yes, I am on the mailing list. Now I can also see that the messages were on
the digest I received, but they did not reach my directly. I don't even see
them in the gmail conversation. Also checked my spam and it's not there...
wired.

On Fri, Jul 30, 2010 at 8:29 PM, Ian Holmes <ih...@be...> wrote:

> David Breimann wrote:
>
>> That;s wired, those mess sages never reached me.
>>
>
> Are you subscribed to the gmod-ajax mailing list? If not, please do so -
>  it may be that you can help the next person who has questions.
>
> Ian
>
>
>
>         Also, I will appreciate a response for my previous message
>>        (cluases 1-5, below).
>>
>>
>>    A few days ago:
>>
>> http://gmod.827538.n3.nabble.com/Gmod-ajax-Formatting-using-GFF-notes-and-some-other-stuff-tp998491p999264.html
>>
>>    Mitch
>>
>
>